Label Coach

Installation Instructions

Requirements

1. Node 8.11.4+
2. mongodb
3. npm 5.6+
4. python 3.6
5. Cairo 1.15 (for canvas)

Step 1: Install girder

Pull girder submodule

cd label-coach
git submodule update --init --recursive

Install all girder python dependencies

cd label-coach/girder
pip install -r requirements-dev.txt

Step 2: Install label_coach plugin

Install all python dependencies.

Linux Distributions

For conda environments use environment.yml in the root directory label-coach

conda env create -n label-coach -f environment.yml
# then activate the conda virtual environment
source activate label-coach

Make sure you have installed openslide-python. Follow installation instructions for openslide and openslide-python installation here : https://openslide.org/download/

OSX

For conda environments use environment.yml in the root directory label-coach

conda env create -n label-coach -f environment.osx.yml
# then activate the conda virtual environment
source activate label-coach

We make use of openslide to support .svs images. To install openslide on OSX you will have to make use of Homebrew

brew install openslide

Install all the npm dependencies inside label_coach dir

cd label-coach/label_coach
npm install

Install plugin into girder. Make sure to provide absolute path to label_coach dir.

girder-install plugin -s /absolute/path/to/label_coach

Step 3: Start up girder and activate plugin. Start mongodb if you havent already.

Install girder web client

sudo service mongod start
girder-install web

Start girder server. Below command will start the server on localhost:8080. check girder documentation for more options

girder serve

Register admin account

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Enable plugin and restart

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Change core_girder route from / to /girder. This setting is found in your Admin console > Server configuration.

Restart the server. You are now all set!

Development Instructions

Step 1: Follow the installation instructions above

Step 2: start webpack watch and server on two seperate terminals

girder-install web --watch-plugin label_coach 

girder serve